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Zhu L, Ma S, He C, Bai L, Tu W, Wu X. Microbial and Metabolic Profiling of Obese and Lean Luchuan Pigs: Implications for Phenotypic Divergence. Animals (Basel) 2024; 14:2111. [PMID: 39061573 PMCID: PMC11273426 DOI: 10.3390/ani14142111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Luchuan (LC) pigs are a Chinese breed renowned for their distinctive black and white coloring, superior meat quality and rapid reproduction, but their growth rate is slow. Over the course of approximately two decades of controlled breeding, the LC pigs maintained at the Shanghai Academy of Agricultural Sciences (Shanghai, China) have diverged into two phenotypes: one characterized by obesity (FLC) and the other by leanness (LLC). Recent studies indicate a correlation between microorganisms and the differentiation of host phenotypes. In this study, we examined the fecal microbiota profiles and serum metabolites of FLC and LLC pigs. The body weight, chest circumference, and alanine aminotransferase and aspartate aminotransferase enzyme activities were increased in the FLC pigs compared to the LLC pigs. Conversely, the levels of the Fusobacterium and Streptococcus genera were lower in the FLC pigs, while the number of Firmicutes, Lactobacillus, Phascolartobacterium, and Rikenellaceae_RC9_gut_group members were higher. A total of 52 metabolites were altered between the two groups, with many playing crucial roles in prolactin signaling, oocyte meiosis, and aldosterone-regulated sodium reabsorption pathways. The correlation analyses demonstrated a significant association between the modified microbiota and metabolites and the phenotypic variations observed in the LC pigs. Specifically, Jeotgalicoccus was positively correlated with the body weight and chest circumference, but was negatively correlated with metabolites such as 2-mercaptobenzothiazole and N1-pyrazin-2-yl-4-chlorobenzamide, which were positively associated with Bacteroides. These results provide compelling evidence for a novel relationship between the gut microbiome and metabolome in the phenotypic differentiation of LC pigs.
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Affiliation(s)
- Lihui Zhu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China;
| | - Shengwei Ma
- Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (S.M.); (C.H.); (L.B.)
| | - Chuan He
- Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (S.M.); (C.H.); (L.B.)
| | - Lan Bai
- Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (S.M.); (C.H.); (L.B.)
| | - Weilong Tu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China;
| | - Xiao Wu
- Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (S.M.); (C.H.); (L.B.)
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2
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Sardar P, Almeida A, Pedicord VA. Integrating functional metagenomics to decipher microbiome-immune interactions. Immunol Cell Biol 2024. [PMID: 38952337 DOI: 10.1111/imcb.12798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/04/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024]
Abstract
Microbial metabolites can be viewed as the cytokines of the microbiome, transmitting information about the microbial and metabolic environment of the gut to orchestrate and modulate local and systemic immune responses. Still, many immunology studies focus solely on the taxonomy and community structure of the gut microbiota rather than its functions. Early sequencing-based microbiota profiling approaches relied on PCR amplification of small regions of bacterial and fungal genomes to facilitate identification of the microbes present. However, recent microbiome analysis methods, particularly shotgun metagenomic sequencing, now enable culture-independent profiling of microbiome functions and metabolites in addition to taxonomic characterization. In this review, we showcase recent advances in functional metagenomics methods and applications and discuss the current limitations and potential avenues for future development. Importantly, we highlight a few examples of key areas of opportunity in immunology research where integrating functional metagenomic analyses of the microbiome can substantially enhance a mechanistic understanding of microbiome-immune interactions and their contributions to health and disease states.
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Affiliation(s)
- Puspendu Sardar
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Alexandre Almeida
- Department of Veterinary Medicine, University of Cambridge School of Biological Sciences, Cambridge, UK
| | - Virginia A Pedicord
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
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3
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Storm MB, Arfaoui EMR, Simelane P, Denlinger J, Dias CA, da Conceição AG, Monadjem A, Bohmann K, Poulsen M, Bodawatta KH. Diet components associated with specific bacterial taxa shape overall gut community compositions in omnivorous African viverrids. Ecol Evol 2024; 14:e11486. [PMID: 39005885 PMCID: PMC11239323 DOI: 10.1002/ece3.11486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 07/16/2024] Open
Abstract
Gut bacterial communities provide flexibility to hosts during dietary changes. Despite the increasing number of studies exploring the associations between broader dietary guilds of mammalian hosts and their gut bacteria, it is generally unclear how diversity and variability in consumed diets link to gut bacterial taxa in wild non-primate mammals, particularly in omnivores. Here, we contribute to filling this gap by exploring consumed diets and gut bacterial community compositions with metabarcoding of faecal samples for two African mammals, Civettictis civetta and Genetta spp., from the family Viverridae. For each individual sample, we characterised bacterial communities and identified dietary taxa by sequencing vertebrate, invertebrate and plant markers. This led us to establish diet compositions that diverged from what has previously been found from visual identification methods. Specifically, while the two genera have been categorised into the same dietary guild, we detected more animal dietary items than plant items in C. civetta, while in Genetta spp., we observed the opposite. We further found that individuals with similar diets have similar gut bacterial communities within both genera. This association tended to be driven by specific links between dietary items and gut bacterial genera, rather than communities as a whole, implying diet-driven selection for specific gut microbes in individual wild hosts. Our findings underline the importance of molecular tools for improving characterisations of omnivorous mammalian diets and highlight the opportunities for simultaneously disentangling links between diets and gut symbionts. Such insights can inform robustness and flexibility in host-microbe symbioses to dietary change associated with seasonal and habitat changes.
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Affiliation(s)
- Malou B. Storm
- Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- Section for Molecular Ecology and EvolutionGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Emilia M. R. Arfaoui
- Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- Section for Molecular Ecology and EvolutionGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Phumlile Simelane
- Department of Biological SciencesUniversity of EswatiniKwaluseniEswatini
| | | | | | | | - Ara Monadjem
- Department of Biological SciencesUniversity of EswatiniKwaluseniEswatini
- Mammal Research Institute, Department of Zoology and EntomologyUniversity of PretoriaHatfield, PretoriaSouth Africa
| | - Kristine Bohmann
- Section for Molecular Ecology and EvolutionGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Kasun H. Bodawatta
- Section for Molecular Ecology and EvolutionGlobe Institute, University of CopenhagenCopenhagenDenmark
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
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4
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Fagan BT, Constable GWA, Law R. Maternal transmission as a microbial symbiont sieve, and the absence of lactation in male mammals. Nat Commun 2024; 15:5341. [PMID: 38937464 PMCID: PMC11211401 DOI: 10.1038/s41467-024-49559-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/11/2024] [Indexed: 06/29/2024] Open
Abstract
Gut microbiomes of mammals carry a complex symbiotic assemblage of microorganisms. Feeding newborn infants milk from the mammary gland allows vertical transmission of the parental milk microbiome to the offspring's gut microbiome. This has benefits, but also has hazards for the host population. Using mathematical models, we demonstrate that biparental vertical transmission enables deleterious microbial elements to invade host populations. In contrast, uniparental vertical transmission acts as a sieve, preventing these invasions. Moreover, we show that deleterious symbionts generate selection on host modifier genes that keep uniparental transmission in place. Since microbial transmission occurs during birth in placental mammals, subsequent transmission of the milk microbiome needs to be maternal to avoid the spread of deleterious elements. This paper therefore argues that viviparity and the hazards from biparental transmission of the milk microbiome, together generate selection against male lactation in placental mammals.
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Affiliation(s)
- Brennen T Fagan
- Leverhulme Centre for Anthropocene Biodiversity, University of York, York, UK.
- Department of Mathematics, University of York, York, UK.
| | | | - Richard Law
- Department of Mathematics, University of York, York, UK
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5
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Buschi E, Dell’Anno A, Tangherlini M, Candela M, Rampelli S, Turroni S, Palladino G, Esposito E, Martire ML, Musco L, Stefanni S, Munari C, Fiori J, Danovaro R, Corinaldesi C. Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome. SCIENCE ADVANCES 2024; 10:eadk9117. [PMID: 38905343 PMCID: PMC11192080 DOI: 10.1126/sciadv.adk9117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
The microbiome plays a key role in the health of all metazoans. Whether and how the microbiome favors the adaptation processes of organisms to extreme conditions, such as those of Antarctica, which are incompatible with most metazoans, is still unknown. We investigated the microbiome of three endemic and widespread species of Antarctic polychaetes: Leitoscoloplos geminus, Aphelochaeta palmeri, and Aglaophamus trissophyllus. We report here that these invertebrates contain a stable bacterial core dominated by Meiothermus and Anoxybacillus, equipped with a versatile genetic makeup and a unique portfolio of proteins useful for coping with extremely cold conditions as revealed by pangenomic and metaproteomic analyses. The close phylosymbiosis between Meiothermus and Anoxybacillus and these Antarctic polychaetes indicates a connection with their hosts that started in the past to support holobiont adaptation to the Antarctic Ocean. The wide suite of bacterial cryoprotective proteins found in Antarctic polychaetes may be useful for the development of nature-based biotechnological applications.
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Affiliation(s)
- Emanuela Buschi
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgia Palladino
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Erika Esposito
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Marco Lo Martire
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Luigi Musco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Sergio Stefanni
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica “Anton Dohrn,” Villa Comunale, Napoli, Italy
| | - Cristina Munari
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Jessica Fiori
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
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6
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Marissen J, Reichert L, Härtel C, Fortmann MI, Faust K, Msanga D, Harder J, Zemlin M, Gomez de Agüero M, Masjosthusmann K, Humberg A. Antimicrobial Peptides (AMPs) and the Microbiome in Preterm Infants: Consequences and Opportunities for Future Therapeutics. Int J Mol Sci 2024; 25:6684. [PMID: 38928389 PMCID: PMC11203687 DOI: 10.3390/ijms25126684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/07/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Antimicrobial peptides (AMPs) are crucial components of the innate immune system in various organisms, including humans. Beyond their direct antimicrobial effects, AMPs play essential roles in various physiological processes. They induce angiogenesis, promote wound healing, modulate immune responses, and serve as chemoattractants for immune cells. AMPs regulate the microbiome and combat microbial infections on the skin, lungs, and gastrointestinal tract. Produced in response to microbial signals, AMPs help maintain a balanced microbial community and provide a first line of defense against infection. In preterm infants, alterations in microbiome composition have been linked to various health outcomes, including sepsis, necrotizing enterocolitis, atopic dermatitis, and respiratory infections. Dysbiosis, or an imbalance in the microbiome, can alter AMP profiles and potentially lead to inflammation-mediated diseases such as chronic lung disease and obesity. In the following review, we summarize what is known about the vital role of AMPs as multifunctional peptides in protecting newborn infants against infections and modulating the microbiome and immune response. Understanding their roles in preterm infants and high-risk populations offers the potential for innovative approaches to disease prevention and treatment.
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Affiliation(s)
- Janina Marissen
- Department of Pediatrics, University Hospital Würzburg, 97080 Würzburg, Germany; (J.M.); (L.R.)
- Würzburg Institute of Systems Immunology, Max-Planck Research Group, University of Würzburg, 97078 Würzburg, Germany;
| | - Lilith Reichert
- Department of Pediatrics, University Hospital Würzburg, 97080 Würzburg, Germany; (J.M.); (L.R.)
| | - Christoph Härtel
- Department of Pediatrics, University Hospital Würzburg, 97080 Würzburg, Germany; (J.M.); (L.R.)
- German Center for Infection Research, Site Hamburg-Lübeck-Borstel-Riems, 23538 Lübeck, Germany
| | - Mats Ingmar Fortmann
- Department of Pediatrics, University Hospital Schleswig-Holstein, 23538 Lübeck, Germany; (M.I.F.); (K.F.)
| | - Kirstin Faust
- Department of Pediatrics, University Hospital Schleswig-Holstein, 23538 Lübeck, Germany; (M.I.F.); (K.F.)
| | - Delfina Msanga
- Department of Pediatrics, Bugando Hospital, Catholic University of Health and Allied Sciences, Mwanza 33109, Tanzania;
| | - Jürgen Harder
- Department of Dermatology, Venerology and Allergology, Quincke Research Center, Kiel University, 24105 Kiel, Germany;
| | - Michael Zemlin
- Department of General Pediatrics and Neonatology, Saarland University Medical Center, 66421 Homburg, Germany;
| | - Mercedes Gomez de Agüero
- Würzburg Institute of Systems Immunology, Max-Planck Research Group, University of Würzburg, 97078 Würzburg, Germany;
| | - Katja Masjosthusmann
- Department of General Pediatrics, University Children’s Hospital Münster, 48149 Münster, Germany; (K.M.); (A.H.)
| | - Alexander Humberg
- Department of General Pediatrics, University Children’s Hospital Münster, 48149 Münster, Germany; (K.M.); (A.H.)
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7
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Ludington WB. The importance of host physical niches for the stability of gut microbiome composition. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230066. [PMID: 38497267 PMCID: PMC10945397 DOI: 10.1098/rstb.2023.0066] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/04/2023] [Indexed: 03/19/2024] Open
Abstract
Gut bacteria are prevalent throughout the Metazoa and form complex microbial communities associated with food breakdown, nutrient provision and disease prevention. How hosts acquire and maintain a consistent bacterial flora remains mysterious even in the best-studied animals, including humans, mice, fishes, squid, bugs, worms and flies. This essay visits the evidence that hosts have co-evolved relationships with specific bacteria and that some of these relationships are supported by specialized physical niches that select, sequester and maintain microbial symbionts. Genetics approaches could uncover the mechanisms for recruiting and maintaining the stable and consistent members of the microbiome. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- William B. Ludington
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Baltimore, MD 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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8
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Maritan E, Quagliariello A, Frago E, Patarnello T, Martino ME. The role of animal hosts in shaping gut microbiome variation. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230071. [PMID: 38497257 PMCID: PMC10945410 DOI: 10.1098/rstb.2023.0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 03/19/2024] Open
Abstract
Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- Elisa Maritan
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Enric Frago
- CIRAD, UMR CBGP, INRAE, Institut Agro, IRD, Université Montpellier, 34398 Montpellier, France
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Maria Elena Martino
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
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9
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Su C, Xie T, Jiang L, Wang Y, Wang Y, Nie R, Zhao Y, He B, Ma J, Yang Q, Hao J. Host genetics and larval host plant modulate microbiome structure and evolution underlying the intimate insect-microbe-plant interactions in Parnassius species on the Qinghai-Tibet Plateau. Ecol Evol 2024; 14:e11218. [PMID: 38606343 PMCID: PMC11007261 DOI: 10.1002/ece3.11218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/09/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
Insects harbor a remarkable diversity of gut microbiomes critical for host survival, health, and fitness, but the mechanism of this structured symbiotic community remains poorly known, especially for the insect group consisting of many closely related species that inhabit the Qinghai-Tibet Plateau. Here, we firstly analyzed population-level 16S rRNA microbial dataset, comprising 11 Parnassius species covering 5 subgenera, from 14 populations mostly sampled in mountainous regions across northwestern-to-southeastern China, and meanwhile clarified the relative importance of multiple factors on gut microbial community structure and evolution. Our findings indicated that both host genetics and larval host plant modulated gut microbial diversity and community structure. Moreover, the effect analysis of host genetics and larval diet on gut microbiomes showed that host genetics played a critical role in governing the gut microbial beta diversity and the symbiotic community structure, while larval host plant remarkably influenced the functional evolution of gut microbiomes. These findings of the intimate insect-microbe-plant interactions jointly provide some new insights into the correlation among the host genetic background, larval host plant, the structure and evolution of gut microbiome, as well as the mechanisms of high-altitude adaptation in closely related species of this alpine butterfly group.
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Affiliation(s)
- Chengyong Su
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Tingting Xie
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Lijun Jiang
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Yunliang Wang
- College of Life SciencesAnhui Normal UniversityWuhuChina
- College of Physical EducationAnhui Normal UniversityWuhuChina
| | - Ying Wang
- College of Life SciencesAnhui Normal UniversityWuhuChina
- College of Physical EducationAnhui Normal UniversityWuhuChina
| | - Ruie Nie
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Youjie Zhao
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Bo He
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Junye Ma
- Key Laboratory of Palaeobiology and Petroleum Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and PaleontologyChinese Academy of SciencesNanjingChina
| | - Qun Yang
- Key Laboratory of Palaeobiology and Petroleum Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and PaleontologyChinese Academy of SciencesNanjingChina
- Nanjing CollegeUniversity of Chinese Academy of SciencesNanjingChina
| | - Jiasheng Hao
- College of Life SciencesAnhui Normal UniversityWuhuChina
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10
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Tedersoo L, Drenkhan R, Abarenkov K, Anslan S, Bahram M, Bitenieks K, Buegger F, Gohar D, Hagh‐Doust N, Klavina D, Makovskis K, Zusevica A, Pritsch K, Padari A, Põlme S, Rahimlou S, Rungis D, Mikryukov V. The influence of tree genus, phylogeny, and richness on the specificity, rarity, and diversity of ectomycorrhizal fungi. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13253. [PMID: 38575147 PMCID: PMC10994715 DOI: 10.1111/1758-2229.13253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
Partner specificity is a well-documented phenomenon in biotic interactions, yet the factors that determine specificity in plant-fungal associations remain largely unknown. By utilizing composite soil samples, we identified the predictors that drive partner specificity in both plants and fungi, with a particular focus on ectomycorrhizal associations. Fungal guilds exhibited significant differences in overall partner preference and avoidance, richness, and specificity to specific tree genera. The highest level of specificity was observed in root endophytic and ectomycorrhizal associations, while the lowest was found in arbuscular mycorrhizal associations. The majority of ectomycorrhizal fungal species showed a preference for one of their partner trees, primarily at the plant genus level. Specialist ectomycorrhizal fungi were dominant in belowground communities in terms of species richness and relative abundance. Moreover, all tree genera (and occasionally species) demonstrated a preference for certain fungal groups. Partner specificity was not related to the rarity of fungi or plants or environmental conditions, except for soil pH. Depending on the partner tree genus, specific fungi became more prevalent and relatively more abundant with increasing stand age, tree dominance, and soil pH conditions optimal for the partner tree genus. The richness of partner tree species and increased evenness of ectomycorrhizal fungi in multi-host communities enhanced the species richness of ectomycorrhizal fungi. However, it was primarily the partner-generalist fungi that contributed to the high diversity of ectomycorrhizal fungi in mixed forests.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
- College of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Rein Drenkhan
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | | | - Sten Anslan
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Mohammad Bahram
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Kriss Bitenieks
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Franz Buegger
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Research Unit Environmental SimulationNeuherbergGermany
| | - Daniyal Gohar
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Niloufar Hagh‐Doust
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Darta Klavina
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Kristaps Makovskis
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Austra Zusevica
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Karin Pritsch
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Research Unit Environmental SimulationNeuherbergGermany
| | - Allar Padari
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Sergei Põlme
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Natural History MuseumUniversity of TartuTartuEstonia
| | - Saleh Rahimlou
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Dainis Rungis
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Vladimir Mikryukov
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
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Zhang M, Zhou Y, Cui X, Zhu L. The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis. Microorganisms 2024; 12:713. [PMID: 38674657 PMCID: PMC11051890 DOI: 10.3390/microorganisms12040713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.
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Affiliation(s)
| | | | | | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing 210098, China; (M.Z.); (Y.Z.); (X.C.)
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12
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Wang S, Gong X, Xiao F, Yang Y. Recent advances in host-focused molecular tools for investigating host-gut microbiome interactions. Front Microbiol 2024; 15:1335036. [PMID: 38605718 PMCID: PMC11007152 DOI: 10.3389/fmicb.2024.1335036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Microbial communities in the human gut play a significant role in regulating host gene expression, influencing a variety of biological processes. To understand the molecular mechanisms underlying host-microbe interactions, tools that can dissect signaling networks are required. In this review, we discuss recent advances in molecular tools used to study this interplay, with a focus on those that explore how the microbiome regulates host gene expression. These tools include CRISPR-based whole-body genetic tools for deciphering host-specific genes involved in the interaction process, Cre-loxP based tissue/cell-specific gene editing approaches, and in vitro models of host-derived organoids. Overall, the application of these molecular tools is revolutionizing our understanding of how host-microbiome interactions contribute to health and disease, paving the way for improved therapies and interventions that target microbial influences on the host.
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Affiliation(s)
- Siyao Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, China
| | - Xu Gong
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, China
| | - Fei Xiao
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Yun Yang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, China
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13
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Tannock GW. Understanding the gut microbiota by considering human evolution: a story of fire, cereals, cooking, molecular ingenuity, and functional cooperation. Microbiol Mol Biol Rev 2024; 88:e0012722. [PMID: 38126754 PMCID: PMC10966955 DOI: 10.1128/mmbr.00127-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
SUMMARYThe microbial community inhabiting the human colon, referred to as the gut microbiota, is mostly composed of bacterial species that, through extensive metabolic networking, degrade and ferment components of food and human secretions. The taxonomic composition of the microbiota has been extensively investigated in metagenomic studies that have also revealed details of molecular processes by which common components of the human diet are metabolized by specific members of the microbiota. Most studies of the gut microbiota aim to detect deviations in microbiota composition in patients relative to controls in the hope of showing that some diseases and conditions are due to or exacerbated by alterations to the gut microbiota. The aim of this review is to consider the gut microbiota in relation to the evolution of Homo sapiens which was heavily influenced by the consumption of a nutrient-dense non-arboreal diet, limited gut storage capacity, and acquisition of skills relating to mastering fire, cooking, and cultivation of cereal crops. The review delves into the past to gain an appreciation of what is important in the present. A holistic view of "healthy" microbiota function is proposed based on the evolutionary pathway shared by humans and gut microbes.
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Affiliation(s)
- Gerald W. Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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14
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Auclert LZ, Chhanda MS, Derome N. Interwoven processes in fish development: microbial community succession and immune maturation. PeerJ 2024; 12:e17051. [PMID: 38560465 PMCID: PMC10981415 DOI: 10.7717/peerj.17051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 02/13/2024] [Indexed: 04/04/2024] Open
Abstract
Fishes are hosts for many microorganisms that provide them with beneficial effects on growth, immune system development, nutrition and protection against pathogens. In order to avoid spreading of infectious diseases in aquaculture, prevention includes vaccinations and routine disinfection of eggs and equipment, while curative treatments consist in the administration of antibiotics. Vaccination processes can stress the fish and require substantial farmer's investment. Additionally, disinfection and antibiotics are not specific, and while they may be effective in the short term, they have major drawbacks in the long term. Indeed, they eliminate beneficial bacteria which are useful for the host and promote the raising of antibiotic resistance in beneficial, commensal but also in pathogenic bacterial strains. Numerous publications highlight the importance that plays the diversified microbial community colonizing fish (i.e., microbiota) in the development, health and ultimately survival of their host. This review targets the current knowledge on the bidirectional communication between the microbiota and the fish immune system during fish development. It explores the extent of this mutualistic relationship: on one hand, the effect that microbes exert on the immune system ontogeny of fishes, and on the other hand, the impact of critical steps in immune system development on the microbial recruitment and succession throughout their life. We will first describe the immune system and its ontogeny and gene expression steps in the immune system development of fishes. Secondly, the plurality of the microbiotas (depending on host organism, organ, and development stage) will be reviewed. Then, a description of the constant interactions between microbiota and immune system throughout the fish's life stages will be discussed. Healthy microbiotas allow immune system maturation and modulation of inflammation, both of which contribute to immune homeostasis. Thus, immune equilibrium is closely linked to microbiota stability and to the stages of microbial community succession during the host development. We will provide examples from several fish species and describe more extensively the mechanisms occurring in zebrafish model because immune system ontogeny is much more finely described for this species, thanks to the many existing zebrafish mutants which allow more precise investigations. We will conclude on how the conceptual framework associated to the research on the immune system will benefit from considering the relations between microbiota and immune system maturation. More precisely, the development of active tolerance of the microbiota from the earliest stages of life enables the sustainable establishment of a complex healthy microbial community in the adult host. Establishing a balanced host-microbiota interaction avoids triggering deleterious inflammation, and maintains immunological and microbiological homeostasis.
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Affiliation(s)
- Lisa Zoé Auclert
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Mousumi Sarker Chhanda
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
- Department of Aquaculture, Faculty of Fisheries, Hajee Mohammad Danesh Science and Technology University, Basherhat, Bangladesh
| | - Nicolas Derome
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
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15
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Song P, Jiang F, Liu D, Cai Z, Gao H, Gu H, Zhang J, Li B, Xu B, Zhang T. Gut microbiota non-convergence and adaptations in sympatric Tibetan and Przewalski's gazelles. iScience 2024; 27:109117. [PMID: 38384851 PMCID: PMC10879710 DOI: 10.1016/j.isci.2024.109117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/17/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Unraveling the connection between gut microbiota and adaptability in wild species in natural habitats is imperative yet challenging. We studied the gut microbiota of sympatric and allopatric populations of two closely related species, the Procapra picticaudata and P. przewalskii, with the latter showing lower adaptability and adaptive potential than the former. Despite shared habitat, sympatric populations showed no convergence in gut microbiota, revealing distinct microbiota-environment relationships between the two gazelle species. Furthermore, the gut microbiota assembly process of the P. przewalskii was shifted toward homogeneous selection processes relative to that of the P. picticaudata. Those taxa which contributed to the shift were mainly from the phyla Firmicutes and Verrucomicrobiota, with functions highly related to micronutrient and macronutrient metabolism. Our study provides new insights into the complex dynamics between gut microbiota, host adaptability, and environment in wildlife adaptation and highlights the need to consider host adaptability when examining wildlife host-microbiome interplay.
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Affiliation(s)
- Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Feng Jiang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Daoxin Liu
- Qinghai University, Xining, Qinghai 810016, China
| | - Zhenyuan Cai
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Hongmei Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Haifeng Gu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Jingjie Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Bin Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Bo Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
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16
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Fong JJ, Sung YH, Ding L. Fine-scale geographic difference of the endangered Big-headed Turtle (Platysternon megacephalum) fecal microbiota, and comparison with the syntopic Beale's Eyed Turtle (Sacalia bealei). BMC Microbiol 2024; 24:71. [PMID: 38418973 PMCID: PMC10902975 DOI: 10.1186/s12866-024-03227-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Studies have elucidated the importance of gut microbiota for an organism, but we are still learning about the important influencing factors. Several factors have been identified in helping shape the microbiome of a host, and in this study we focus on two factors-geography and host. We characterize the fecal microbiota of the Big-headed Turtle (Platysternon megacephalum) and compare across a relatively fine geographic scale (three populations within an 8-km radius) and between two syntopic hosts (P. megacephalum and Sacalia bealei). Both species are endangered, which limits the number of samples we include in the study. Despite this limitation, these data serve as baseline data for healthy, wild fecal microbiotas of two endangered turtle species to aid in conservation management. RESULTS For geography, the beta diversity of fecal microbiota differed between the most distant sites. The genus Citrobacter significantly differs between sites, which may indicate a difference in food availability, environmental microbiota, or both. Also, we identify the common core microbiome for Platysternon across Hong Kong as the shared taxa across the three sites. Additionally, beta diversity differs between host species. Since the two species are from the same site and encounter the same environmental microbiota, we infer that there is a host effect on the fecal microbiota, such as diet or the recruitment of host-adapted bacteria. Lastly, functional analyses found metabolism pathways (KEGG level 1) to be the most common, and pathways (KEGG level 3) to be statistically significant between sites, but statistically indistinguishable between species at the same site. CONCLUSIONS We find that fecal microbiota can significantly differ at a fine geographic scale and between syntopic hosts. Also, the function of fecal microbiota seems to be strongly affected by geographic site, rather than species. This study characterizes the identity and function of the fecal microbiota of two endangered turtle species, from what is likely their last remaining wild populations. These data of healthy, wild fecal microbiota will serve as a baseline for comparison and contribute to the conservation of these two endangered species.
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Affiliation(s)
| | - Yik-Hei Sung
- Science Unit, Lingnan University, Hong Kong, China
- School of Allied Health Sciences, University of Suffolk, 19 Neptune Quay, Ipswich, IP4 1QJ, UK
| | - Li Ding
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China.
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17
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Soh M, Tay YC, Lee CS, Low A, Orban L, Jaafar Z, Seedorf H. The intestinal digesta microbiota of tropical marine fish is largely uncultured and distinct from surrounding water microbiota. NPJ Biofilms Microbiomes 2024; 10:11. [PMID: 38374184 PMCID: PMC10876542 DOI: 10.1038/s41522-024-00484-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Studying the gut microbes of marine fishes is an important part of conservation as many fish species are increasingly threatened by extinction. The gut microbiota of only a small fraction of the more than 32,000 known fish species has been investigated. In this study we analysed the intestinal digesta microbiota composition of more than 50 different wild fish species from tropical waters. Our results show that the fish harbour intestinal digesta microbiota that are distinct from that of the surrounding water and that location, domestication status, and host intrinsic factors are strongly associated with the microbiota composition. Furthermore, we show that the vast majority (~97%) of the fish-associated microorganisms do not have any cultured representative. Considering the impact of the microbiota on host health and physiology, these findings underpin the call to also preserve the microbiota of host species, especially those that may be exposed to habitat destruction.
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Affiliation(s)
- Melissa Soh
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Ywee Chieh Tay
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Co Sin Lee
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Adrian Low
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, MD6-Centre for Translational Medicine, 14 Medical Drive, Singapore, 117599, Singapore
| | - Laszlo Orban
- Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, Keszthely, 8360, Hungary
| | - Zeehan Jaafar
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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18
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Plata G, Krishnamurthy M, Herron L, Dixit P. Designing host-associated microbiomes using the consumer/resource model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.28.538625. [PMID: 37162888 PMCID: PMC10168316 DOI: 10.1101/2023.04.28.538625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A key step towards rational microbiome engineering is the in silico sampling of realistic microbial communities that correspond to desired host phenotypes, and vice versa. This remains challenging due to a lack of generative models that simultaneously model compositions of host-associated microbiomes and host phenotypes. To that end, we present a machine learning model based on the consumer/resource (C/R) framework. In the model, variation in microbial ecosystem composition arises due to differences in the availability of effective resources (latent variables) while species' resource preferences remain conserved. Variation in the same latent variables is used to model phenotypic variation across hosts. In silico microbiomes generated by our model accurately reproduce universal and dataset-specific statistics of bacterial communities. The model allows us to address two salient questions in microbiome design: (1) which host phenotypes maximally constrain the composition of the host-associated microbiome? and (2) what are plausible microbiome compositions corresponding to user-specified host phenotypes? Thus, our model aids the design and analysis of microbial communities associated with host phenotypes of interest.
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19
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Mazel F, Pitteloud C, Guisan A, Pellissier L. Contrasted host specificity of gut and endosymbiont bacterial communities in alpine grasshoppers and crickets. ISME COMMUNICATIONS 2024; 4:ycad013. [PMID: 38374896 PMCID: PMC10875604 DOI: 10.1093/ismeco/ycad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024]
Abstract
Bacteria colonize the body of macroorganisms to form associations ranging from parasitic to mutualistic. Endosymbiont and gut symbiont communities are distinct microbiomes whose compositions are influenced by host ecology and evolution. Although the composition of horizontally acquired symbiont communities can correlate to host species identity (i.e. harbor host specificity) and host phylogeny (i.e. harbor phylosymbiosis), we hypothesize that the microbiota structure of vertically inherited symbionts (e.g. endosymbionts like Wolbachia) is more strongly associated with the host species identity and phylogeny than horizontally acquired symbionts (e.g. most gut symbionts). Here, using 16S metabarcoding on 336 guts from 24 orthopteran species (grasshoppers and crickets) in the Alps, we observed that microbiota correlated to host species identity, i.e. hosts from the same species had more similar microbiota than hosts from different species. This effect was ~5 times stronger for endosymbionts than for putative gut symbionts. Although elevation correlated with microbiome composition, we did not detect phylosymbiosis for endosymbionts and putative gut symbionts: closely related host species did not harbor more similar microbiota than distantly related species. Our findings indicate that gut microbiota of studied orthopteran species is more correlated to host identity and habitat than to the host phylogeny. The higher host specificity in endosymbionts corroborates the idea that-everything else being equal-vertically transmitted microbes harbor stronger host specificity signal, but the absence of phylosymbiosis suggests that host specificity changes quickly on evolutionary time scales.
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Affiliation(s)
- Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Camille Pitteloud
- Département de la mobilité, du territoire et de l'environnement, Service des forêts, de la nature et du paysage, Sion 1950, Switzerland
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne 1015, Switzerland
| | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
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20
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Rose C, Lund MB, Schramm A, Bilde T, Bechsgaard J. Does ecological drift explain variation in microbiome composition among groups in a social host species? J Evol Biol 2023; 36:1684-1694. [PMID: 37776090 DOI: 10.1111/jeb.14228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/18/2023] [Accepted: 06/26/2023] [Indexed: 10/01/2023]
Abstract
Within a given species, considerable inter-individual, spatial, and temporal variation in the composition of the host microbiome exists. In group-living animals, social interactions homogenize microbiome composition among group members, nevertheless divergence in microbiome composition among related groups arise. Such variation can result from deterministic and stochastic processes. Stochastic changes, or ecological drift, can occur among symbionts with potential for colonizing a host and within individual hosts, and drive divergence in microbiome composition among hosts or host groups. We tested whether ecological drift associated with dispersal and foundation of new groups cause divergence in microbiome composition between natal and newly formed groups in the social spider Stegodyphus dumicola. We simulated the initiation of new groups by splitting field-collected nests into groups of 1, 3, and 10 individuals respectively, and compared variation in microbiome composition among and within groups after 6 weeks using 16S rRNA gene sequencing. Theory predicts that ecological drift increases with decreasing group size. We found that microbiome composition among single founders was more dissimilar than among individuals kept in groups, supporting this prediction. Divergence in microbiome composition from the natal nest was mainly driven by a higher number of non-core symbionts. This suggests that stochastic divergence in host microbiomes can arise during the process of group formation by individual founders, which could explain the existence of among-group variation in microbiome composition in the wild. Individual founders appear to harbour higher relative abundances of non-core symbionts compared with founders in small groups, some of which are possible pathogens. These symbionts vary in occurrence with group size, indicating that group dynamics influence various core and non-core symbionts differently.
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Affiliation(s)
- Clémence Rose
- Section for Genetic Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Marie Braad Lund
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Trine Bilde
- Section for Genetic Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Jesper Bechsgaard
- Section for Genetic Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
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21
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Sadeghi J, Chaganti SR, Johnson TB, Heath DD. Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome. MICROBIOME 2023; 11:258. [PMID: 37981701 PMCID: PMC10658978 DOI: 10.1186/s40168-023-01697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/11/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (hereafter referred to as microbiota) and assess the extent to which host habitat and phylogeny predict microbiota similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario). We also collected and filtered water samples at the time of fish collection. We analyzed bacterial community composition using 16S metabarcoding and tested for community variation. RESULTS We found that the water microbiota was distinct from the fish microbiota, although the skin microbiota more closely resembled the water microbiota. We also found that environmental (sample location), habitat, fish diet, and host species factors shape and promote divergence or convergence of the fish microbiota. Since host species significantly affected both gut and skin microbiota (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus bacterial community dissimilarity. We found significant phylogenetic effects on bacterial community dissimilarity, consistent with phylosymbiosis for both the fish skin and gut microbiota, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes. CONCLUSIONS Analyzing the gut and skin mucus microbiota across diverse fish species in complex natural ecosystems such as the LGLs provides insights into the potential for habitat and species-specific effects on the microbiome, and ultimately the health, of the host. Video Abstract.
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Affiliation(s)
- Javad Sadeghi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, USA
| | - Timothy B Johnson
- Ontario Ministry of Natural Resources and Forestry, Glenora Fisheries Station, Picton, ON, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada.
- Department of Integrative Biology, University of Windsor, Windsor, ON, Canada.
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22
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Qin M, Jiang L, Qiao G, Chen J. Phylosymbiosis: The Eco-Evolutionary Pattern of Insect-Symbiont Interactions. Int J Mol Sci 2023; 24:15836. [PMID: 37958817 PMCID: PMC10650905 DOI: 10.3390/ijms242115836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Insects harbor diverse assemblages of bacterial and fungal symbionts, which play crucial roles in host life history. Insects and their various symbionts represent a good model for studying host-microbe interactions. Phylosymbiosis is used to describe an eco-evolutionary pattern, providing a new cross-system trend in the research of host-associated microbiota. The phylosymbiosis pattern is characterized by a significant positive correlation between the host phylogeny and microbial community dissimilarities. Although host-symbiont interactions have been demonstrated in many insect groups, our knowledge of the prevalence and mechanisms of phylosymbiosis in insects is still limited. Here, we provide an order-by-order summary of the phylosymbiosis patterns in insects, including Blattodea, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera. Then, we highlight the potential contributions of stochastic effects, evolutionary processes, and ecological filtering in shaping phylosymbiotic microbiota. Phylosymbiosis in insects can arise from a combination of stochastic and deterministic mechanisms, such as the dispersal limitations of microbes, codiversification between symbionts and hosts, and the filtering of phylogenetically conserved host traits (incl., host immune system, diet, and physiological characteristics).
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Affiliation(s)
- Man Qin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (M.Q.); (L.J.)
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (M.Q.); (L.J.)
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (M.Q.); (L.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (M.Q.); (L.J.)
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23
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Teullet S, Tilak MK, Magdeleine A, Schaub R, Weyer NM, Panaino W, Fuller A, Loughry WJ, Avenant NL, de Thoisy B, Borrel G, Delsuc F. Metagenomics uncovers dietary adaptations for chitin digestion in the gut microbiota of convergent myrmecophagous mammals. mSystems 2023; 8:e0038823. [PMID: 37650612 PMCID: PMC10654083 DOI: 10.1128/msystems.00388-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/19/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE Myrmecophagous mammals are specialized in the consumption of ants and/or termites. They do not share a direct common ancestor and evolved convergently in five distinct placental orders raising questions about the underlying adaptive mechanisms involved and the relative contribution of natural selection and phylogenetic constraints. Understanding how these species digest their prey can help answer these questions. More specifically, the role of their gut microbial symbionts in the digestion of the insect chitinous exoskeleton has not been investigated in all myrmecophagous orders. We generated 29 new gut metagenomes from nine myrmecophagous species to reconstruct more than 300 bacterial genomes in which we identified chitin-degrading enzymes. Studying the distribution of these chitinolytic bacteria among hosts revealed both shared and specific bacteria between ant-eating species. Overall, our results highlight the potential role of gut symbionts in the convergent dietary adaptation of myrmecophagous mammals and the evolutionary mechanisms shaping their gut microbiota.
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Affiliation(s)
- Sophie Teullet
- Institut des Sciences de l’Evolution de Montpellier (ISEM), Univ Montpellier, CNRS, IRD, Montpellier, France
| | - Marie-Ka Tilak
- Institut des Sciences de l’Evolution de Montpellier (ISEM), Univ Montpellier, CNRS, IRD, Montpellier, France
| | - Amandine Magdeleine
- Institut des Sciences de l’Evolution de Montpellier (ISEM), Univ Montpellier, CNRS, IRD, Montpellier, France
| | - Roxane Schaub
- CIC AG/Inserm 1424, Centre Hospitalier de Cayenne Andrée Rosemon, Cayenne, French Guiana, France
- Tropical Biome and immunopathology, Université de Guyane, Labex CEBA, DFR Santé, Cayenne, French Guiana, France
| | - Nora M. Weyer
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
| | - Wendy Panaino
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for African Ecology, School of Animals, Plant, and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrea Fuller
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
| | - W. J. Loughry
- Department of Biology, Valdosta State University, Valdosta, Georgia, USA
| | - Nico L. Avenant
- National Museum and Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa
| | - Benoit de Thoisy
- Institut Pasteur de la Guyane, Cayenne, French Guiana, France
- Kwata NGO, Cayenne, French Guiana, France
| | - Guillaume Borrel
- Evolutionary Biology of the Microbial Cell, Institut Pasteur, Université Paris Cité, Paris, France
| | - Frédéric Delsuc
- Institut des Sciences de l’Evolution de Montpellier (ISEM), Univ Montpellier, CNRS, IRD, Montpellier, France
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24
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Yin R, Wang T, Dai H, Han J, Sun J, Liu N, Dong W, Zhong J, Liu H. Immunogenic molecules associated with gut bacterial cell walls: chemical structures, immune-modulating functions, and mechanisms. Protein Cell 2023; 14:776-785. [PMID: 37013853 PMCID: PMC10599643 DOI: 10.1093/procel/pwad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 03/25/2023] [Indexed: 04/05/2023] Open
Abstract
Interactions between gut microbiome and host immune system are fundamental to maintaining the intestinal mucosal barrier and homeostasis. At the host-gut microbiome interface, cell wall-derived molecules from gut commensal bacteria have been reported to play a pivotal role in training and remodeling host immune responses. In this article, we review gut bacterial cell wall-derived molecules with characterized chemical structures, including peptidoglycan and lipid-related molecules that impact host health and disease processes via regulating innate and adaptive immunity. Also, we aim to discuss the structures, immune responses, and underlying mechanisms of these immunogenic molecules. Based on current advances, we propose cell wall-derived components as important sources of medicinal agents for the treatment of infection and immune diseases.
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Affiliation(s)
- Ruopeng Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huanqin Dai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junjie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingzu Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ningning Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wang Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Hongwei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
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25
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Zhang XY, Khakisahneh S, Liu W, Zhang X, Zhai W, Cheng J, Speakman JR, Wang DH. Phylogenetic signal in gut microbial community rather than in rodent metabolic traits. Natl Sci Rev 2023; 10:nwad209. [PMID: 37928774 PMCID: PMC10625476 DOI: 10.1093/nsr/nwad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 11/07/2023] Open
Abstract
Host phylogeny and environment have all been implicated in shaping the gut microbiota and host metabolic traits of mammals. However, few studies have evaluated phylogeny-associated microbial assembly and host metabolic plasticity concurrently, and their relationships on both short-term and evolutionary timescales. We report that the branching order of a gut microbial dendrogram was nearly congruent with phylogenetic relationships of seven rodent species, and this pattern of phylosymbiosis was intact after diverse laboratory manipulations. Laboratory rearing, diet or air temperature (Ta) acclimation induced alterations in gut microbial communities, but could not override host phylogeny in shaping microbial community assembly. A simulative heatwave reduced core microbiota diversity by 26% in these species, and led to an unmatched relationship between the microbiota and host metabolic phenotypes in desert species. Moreover, the similarity of metabolic traits across species at different Tas was not correlated with phylogenetic distance. These data demonstrated that the gut microbial assembly showed strong concordance with host phylogeny and may be shaped by environmental variables, whereas host metabolic traits did not seem to be linked with phylogeny.
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Affiliation(s)
- Xue-Ying Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Saeid Khakisahneh
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinyi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - John R Speakman
- Shenzhen Key Laboratory of Metabolic Health, Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB39 2PN, UK
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - De-Hua Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, Shandong University, Qingdao 266237, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
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26
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Malard LA, Guisan A. Into the microbial niche. Trends Ecol Evol 2023; 38:936-945. [PMID: 37236880 DOI: 10.1016/j.tree.2023.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023]
Abstract
The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.
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Affiliation(s)
- Lucie A Malard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Institute of Earth Surface Dynamics, University of Lausanne, 1015 Lausanne, Switzerland
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27
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Rios Galicia B, Sáenz JS, Yergaliyev T, Camarinha-Silva A, Seifert J. Host specific adaptations of Ligilactobacillus aviarius to poultry. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 5:100199. [PMID: 37727231 PMCID: PMC10505982 DOI: 10.1016/j.crmicr.2023.100199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
Abstract
The genus Ligilactobacillus encompasses species adapted to vertebrate hosts and fermented food. Their genomes encode adaptations to the host lifestyle. Reports of gut microbiota from chicken and turkey gastrointestinal tract have shown a high persistence of Ligilactobacillus aviarius along the digestive system compared to other species found in the same host. However, its adaptations to poultry as a host has not yet been described. In this work, the pan-genome of Ligilactobacillus aviarius was explored to describe the functional adaptability to the gastrointestinal environment. The core genome is composed of 1179 gene clusters that are present at least in one copy that codifies to structural, ribosomal and biogenesis proteins. The rest of the identified regions were classified into three different functional clusters of orthologous groups (clusters) that codify carbohydrate metabolism, envelope biogenesis, viral defence mechanisms, and mobilome inclusions. The pan-genome of Ligilactobacillus aviarius is a closed pan-genome, frequently found in poultry and highly prevalent across chicken faecal samples. The genome of L. aviarius codifies different clusters of glycoside hydrolases and glycosyltransferases that mediate interactions with the host cells. Accessory features, such as antiviral mechanisms and prophage inclusions, variate amongst strains from different GIT sections. This information provides hints about the interaction of this species with viral particles and other bacterial species. This work highlights functional adaptability traits present in L. aviarius that make it a dominant key member of the poultry gut microbiota and enlightens the convergent ecological relation of this species to the poultry gut environment.
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Affiliation(s)
- Bibiana Rios Galicia
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, Stuttgart 70593, Germany
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, Stuttgart 70593, Germany
| | - Johan Sebastian Sáenz
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, Stuttgart 70593, Germany
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, Stuttgart 70593, Germany
| | - Timur Yergaliyev
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, Stuttgart 70593, Germany
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, Stuttgart 70593, Germany
| | - Amélia Camarinha-Silva
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, Stuttgart 70593, Germany
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, Stuttgart 70593, Germany
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, Stuttgart 70593, Germany
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, Stuttgart 70593, Germany
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28
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Zhou Y, Duan L, Zeng Y, Song X, Pan K, Niu L, Pu Y, Li J, Khalique A, Fang J, Jing B, Zeng D, Shen B, Ni X. The panda-derived Lactiplantibacillus plantarum BSG201683 improves LPS-induced intestinal inflammation and epithelial barrier disruption in vitro. BMC Microbiol 2023; 23:249. [PMID: 37674107 PMCID: PMC10481503 DOI: 10.1186/s12866-023-02928-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/03/2023] [Indexed: 09/08/2023] Open
Abstract
Captive pandas are suffering from intestinal infection due to intestinal microbiota characterized by a high abundance of Enterobacteriaceae induced by long-term captivity. Probiotic supplements showed improvement in intestinal barrier function and inflammation. However, the effects of panda-derived probiotics on the intestinal epithelium and inflammation have not been elucidated. In the present study, lipopolysaccharide (LPS) impaired Caco-2 and RAW264.7 inflammatory models were applied to assess the protection of Lactiplantibacillus plantarum BSG201683 (L. plantarum G83) on barrier disruption and inflammation. The results showed that treatment with L. plantarum G83 significantly decreased the paracellular permeability to fluorescein isothiocyanate conjugated dextran (MW 4000, FITC-D4) after LPS induction. Meanwhile, L. plantarum G83 alleviated the reduction in tight junction (TJ) proteins and downregulated proinflammatory cytokines caused by LPS in Caco-2 cells. L. plantarum G83 also significantly decreased the expression and secretion of pro-inflammatory cytokines in LPS-induced RAW264.7 cells. In addition, the IL-10 increased in both Caco-2 and RAW264.7 cells after L. plantarum G83 treatment. The phagocytosis activity of RAW264.7 cells was significantly increased after L. plantarum G83 treatment. Toll-like receptor 4/ nuclear factor kappa-B (TLR4/NF-κB) signaling pathways were significantly down-regulated after L. plantarum G83 intervention, and the phosphorylation of NF-κB/p65 was consistent with this result. Our findings suggest that L. plantarum G83 improves intestinal inflammation and epithelial barrier disruption in vitro.
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Affiliation(s)
- Yi Zhou
- Animal Microecology Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 611130, Sichuan, China
| | - Ling Duan
- Animal Feed Affairs of Sichuan Province, Sichuan Provincial Department of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan, China
| | - Yan Zeng
- Animal Microecology Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xu Song
- Animal Microecology Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Kangcheng Pan
- Animal Microecology Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lili Niu
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, 610081, Sichuan, China
| | - Yang Pu
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, 610081, Sichuan, China
| | - Jiakun Li
- Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 611130, Sichuan, China
| | - Abdul Khalique
- Animal Microecology Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jing Fang
- Animal Microecology Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Bo Jing
- Animal Microecology Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dong Zeng
- Animal Microecology Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Bairong Shen
- Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 611130, Sichuan, China.
| | - Xueqin Ni
- Animal Microecology Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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29
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Keady MM, Jimenez RR, Bragg M, Wagner JCP, Bornbusch SL, Power ML, Muletz-Wolz CR. Ecoevolutionary processes structure milk microbiomes across the mammalian tree of life. Proc Natl Acad Sci U S A 2023; 120:e2218900120. [PMID: 37399384 PMCID: PMC10334807 DOI: 10.1073/pnas.2218900120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 05/22/2023] [Indexed: 07/05/2023] Open
Abstract
Milk production is an ancient adaptation that unites all mammals. Milk contains a microbiome that can contribute to offspring health and microbial-immunological development. We generated a comprehensive milk microbiome dataset (16S rRNA gene) for the class Mammalia, representing 47 species from all placental superorders, to determine processes structuring milk microbiomes. We show that across Mammalia, milk exposes offspring to maternal bacterial and archaeal symbionts throughout lactation. Deterministic processes of environmental selection accounted for 20% of milk microbiome assembly processes; milk microbiomes were similar from mammals with the same host superorder (Afrotheria, Laurasiathera, Euarchontoglires, and Xenarthra: 6%), environment (marine captive, marine wild, terrestrial captive, and terrestrial wild: 6%), diet (carnivore, omnivore, herbivore, and insectivore: 5%), and milk nutrient content (sugar, fat, and protein: 3%). We found that diet directly and indirectly impacted milk microbiomes, with indirect effects being mediated by milk sugar content. Stochastic processes, such as ecological drift, accounted for 80% of milk microbiome assembly processes, which was high compared to mammalian gut and mammalian skin microbiomes (69% and 45%, respectively). Even amid high stochasticity and indirect effects, our results of direct dietary effects on milk microbiomes provide support for enteromammary trafficking, representing a mechanism by which bacteria are transferred from the mother's gut to mammary gland and then to offspring postnatally. The microbial species present in milk reflect both selective pressures and stochastic processes at the host level, exemplifying various ecological and evolutionary factors acting on milk microbiomes, which, in turn, set the stage for offspring health and development.
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Affiliation(s)
- Mia M. Keady
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC20008
- Nelson Institute for Environmental Studies, University of Wisconsin-Madison, Madison, WI53706
| | - Randall R. Jimenez
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC20008
- Science Team, International Union for Conservation of Nature, 11501San José, Costa Rica
| | - Morgan Bragg
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC20008
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA22030
| | - Jenna C. P. Wagner
- Nutrition Laboratory and Conservation Ecology Center, Smithsonian National Zoo and Conservation Biology Institute, National Zoological Park, Washington, DC20008
| | - Sally L. Bornbusch
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC20008
- Department of Nutrition Science, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC20008
| | - Michael L. Power
- Nutrition Laboratory and Conservation Ecology Center, Smithsonian National Zoo and Conservation Biology Institute, National Zoological Park, Washington, DC20008
| | - Carly R. Muletz-Wolz
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC20008
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30
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Sprockett DD, Price JD, Juritsch AF, Schmaltz RJ, Real MV, Goldman SL, Sheehan M, Ramer-Tait AE, Moeller AH. Home-site advantage for host species-specific gut microbiota. SCIENCE ADVANCES 2023; 9:eadf5499. [PMID: 37184968 PMCID: PMC10184861 DOI: 10.1126/sciadv.adf5499] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/06/2023] [Indexed: 05/17/2023]
Abstract
Mammalian species harbor compositionally distinct gut microbial communities, but the mechanisms that maintain specificity of symbionts to host species remain unclear. Here, we show that natural selection within house mice (Mus musculus domesticus) drives deterministic assembly of the house-mouse gut microbiota from mixtures of native and non-native microbiotas. Competing microbiotas from wild-derived lines of house mice and other mouse species (Mus and Peromyscus spp.) within germ-free wild-type (WT) and Rag1-knockout (Rag1-/-) house mice revealed widespread fitness advantages for native gut bacteria. Native bacterial lineages significantly outcompeted non-native lineages in both WT and Rag1-/- mice, indicating home-site advantage for native microbiota independent of host adaptive immunity. However, a minority of native Bacteriodetes and Firmicutes favored by selection in WT hosts were not favored or disfavored in Rag1-/- hosts, indicating that Rag1 mediates fitness advantages of these strains. This study demonstrates home-site advantage for native gut bacteria, consistent with local adaptation of gut microbiota to their mammalian species.
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Affiliation(s)
- Daniel D. Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jeffrey D. Price
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Anthony F. Juritsch
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Robert J. Schmaltz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Madalena V. F. Real
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Samantha L. Goldman
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Michael Sheehan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Amanda E. Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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31
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Chai Y, Huang Z, Shen X, Lin T, Zhang Y, Feng X, Mao Q, Liang Y. Microbiota Regulates Pancreatic Cancer Carcinogenesis through Altered Immune Response. Microorganisms 2023; 11:1240. [PMID: 37317214 PMCID: PMC10221276 DOI: 10.3390/microorganisms11051240] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 06/16/2023] Open
Abstract
The microbiota is present in many parts of the human body and plays essential roles. The most typical case is the occurrence and development of cancer. Pancreatic cancer (PC), one of the most aggressive and lethal types of cancer, has recently attracted the attention of researchers. Recent research has revealed that the microbiota regulates PC carcinogenesis via an altered immune response. Specifically, the microbiota, in several sites, including the oral cavity, gastrointestinal tract, and pancreatic tissue, along with the numerous small molecules and metabolites it produces, influences cancer progression and treatment by activating oncogenic signaling, enhancing oncogenic metabolic pathways, altering cancer cell proliferation, and triggering chronic inflammation that suppresses tumor immunity. Diagnostics and treatments based on or in combination with the microbiota offer novel insights to improve efficiency compared with existing therapies.
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Affiliation(s)
- Yihan Chai
- Department of General Surgery, Zhejiang University School of Medicine, Sir Run Run Shaw Hospital, Hangzhou 310016, China
| | - Zhengze Huang
- Department of General Surgery, Zhejiang University School of Medicine, Sir Run Run Shaw Hospital, Hangzhou 310016, China
| | - Xuqiu Shen
- Department of General Surgery, Zhejiang University School of Medicine, Sir Run Run Shaw Hospital, Hangzhou 310016, China
| | - Tianyu Lin
- Department of General Surgery, Zhejiang University School of Medicine, Sir Run Run Shaw Hospital, Hangzhou 310016, China
| | - Yiyin Zhang
- Department of General Surgery, Zhejiang University School of Medicine, Sir Run Run Shaw Hospital, Hangzhou 310016, China
| | - Xu Feng
- Department of General Surgery, Zhejiang University School of Medicine, Sir Run Run Shaw Hospital, Hangzhou 310016, China
| | - Qijiang Mao
- Department of General Surgery, Zhejiang University School of Medicine, Sir Run Run Shaw Hospital, Hangzhou 310016, China
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Hangzhou 310016, China
- Zhejiang Province Medical Research Center of Minimally Invasive Diagnosis and Treatment of Abdominal Diseases, Hangzhou 310028, China
| | - Yuelong Liang
- Department of General Surgery, Zhejiang University School of Medicine, Sir Run Run Shaw Hospital, Hangzhou 310016, China
- Zhejiang Province Medical Research Center of Minimally Invasive Diagnosis and Treatment of Abdominal Diseases, Hangzhou 310028, China
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Yang P, Zhu X, Ning K. Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function relationship. Commun Biol 2023; 6:391. [PMID: 37037946 PMCID: PMC10085995 DOI: 10.1038/s42003-023-04753-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 03/24/2023] [Indexed: 04/12/2023] Open
Abstract
Microbes live in diverse habitats (i.e. biomes), yet their species and genes were biome-specific, forming enrichment patterns. These enrichment patterns have mirrored the biome-species-function relationship, which is shaped by ecological and evolutionary principles. However, a grand picture of these enrichment patterns, as well as the roles of external and internal factors in driving these enrichment patterns, remain largely unexamined. In this work, we have examined the enrichment patterns based on 1705 microbiome samples from four representative biomes (Engineered, Gut, Freshwater, and Soil). Moreover, an "enrichment sphere" model was constructed to elucidate the regulatory principles behind these patterns. The driving factors for this model were revealed based on two case studies: (1) The copper-resistance genes were enriched in Soil biomes, owing to the copper contamination and horizontal gene transfer. (2) The flagellum-related genes were enriched in the Freshwater biome, due to high fluidity and vertical gene accumulation. Furthermore, this enrichment sphere model has valuable applications, such as in biome identification for metagenome samples, and in guiding 3D structure modeling of proteins. In summary, the enrichment sphere model aims towards creating a bluebook of the biome-species-function relationships and be applied in many fields.
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Affiliation(s)
- Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Institute of Medical Genomics, Biomedical Sciences College, Shandong First Medical University, Shandong, 250117, China
| | - Xue Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Institute of Medical Genomics, Biomedical Sciences College, Shandong First Medical University, Shandong, 250117, China.
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Li H, Xia W, Liu X, Wang X, Liu G, Chen H, Zhu L, Li D. Food provisioning results in functional, but not compositional, convergence of the gut microbiomes of two wild Rhinopithecus species: Evidence of functional redundancy in the gut microbiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159957. [PMID: 36343820 DOI: 10.1016/j.scitotenv.2022.159957] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
The consumption of similar diets has led to the convergence of gut microbial compositions and functions across phylogenetically distinct animals. However, given the functional redundancy in gut microbiomes, it remains unclear whether synchrony occurs in their functions only and not in their composition, even within phylogenetically close animals consuming a similar diet. In this study, we collected fresh fecal samples from a Rhinopithecus roxellana population in April 2021 (before food provisioning) and June and December 2021 (after food provisioning) and used high-throughput sequencing methods (full-length 16S rRNA gene sequencing and metagenomes) to investigate changes in the gut microbiome due to food provisioning. Combining the results from our previous studies on a wild Rhinopithecus bieti population, we found that the artificial food provisions (e.g., apples, carrots, and peanuts) affected the gut microbiome, and synchrony occurred only in its functions and antibiotic resistance gene community in both Rhinopithecus species, reflecting its ecological functional redundancy. Given the current findings (e.g., depletion in probiotic microbes, dysbiosis in the gut microbial community, and changes in the antibiotic resistance gene profile), anthropogenic disturbances (e.g., food provisioning) would have potential negative effects on host health. Therefore, human activity in animal conservation should be rethought from the standpoint of gut microbial diversity.
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Affiliation(s)
- Hong Li
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China; Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Wancai Xia
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China
| | - Xingyu Liu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China
| | - Xueyu Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China
| | - Guoqi Liu
- Mingke Biotechnology, Hangzhou, China
| | - Hua Chen
- Mingke Biotechnology, Hangzhou, China
| | - Lifeng Zhu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Dayong Li
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China.
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Baldo L, Tavecchia G, Rotger A, Igual JM, Riera JL. Insular holobionts: persistence and seasonal plasticity of the Balearic wall lizard ( Podarcis lilfordi) gut microbiota. PeerJ 2023; 11:e14511. [PMID: 36620745 PMCID: PMC9817956 DOI: 10.7717/peerj.14511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/14/2022] [Indexed: 01/04/2023] Open
Abstract
Background Integrative studies of animals and associated microbial assemblages (i.e., the holobiont) are rapidly changing our perspectives on organismal ecology and evolution. Insular vertebrates provide ideal natural systems to understand patterns of host-gut microbiota coevolution, the resilience and plasticity these microbial communities over temporal and spatial scales, and ultimately their role in the host ecological adaptation. Methods Here we used the endemic Balearic wall lizard Podarcis lilfordi to dissect the drivers of the microbial diversity within and across host allopatric populations/islets. By focusing on three extensively studied populations/islets of Mallorca (Spain) and fecal sampling from individually identified lizards along two years (both in spring and autumn), we sorted out the effect of islet, sex, life stage, year and season on the microbiota composition. We further related microbiota diversity to host genetics, trophic ecology and expected annual metabolic changes. Results All the three populations showed a remarkable conservation of the major microbial taxonomic profile, while carrying their unique microbial signature at finer level of taxonomic resolution (Amplicon Sequence Variants (ASVs)). Microbiota distances across populations were compatible with both host genetics (based on microsatellites) and trophic niche distances (based on stable isotopes and fecal content). Within populations, a large proportion of ASVs (30-50%) were recurrently found along the four sampling dates. The microbial diversity was strongly marked by seasonality, with no sex effect and a marginal life stage and annual effect. The microbiota showed seasonal fluctuations along the two sampled years, primarily due to changes in the relative abundances of fermentative bacteria (mostly families Lachnospiraceae and Ruminococcaceae), without any major compositional turnover. Conclusions These results support a large resilience of the major compositional aspects of the P. lilfordi gut microbiota over the short-term evolutionary divergence of their host allopatric populations (<10,000 years), but also indicate an undergoing process of parallel diversification of the both host and associated gut microbes. Predictable seasonal dynamics in microbiota diversity suggests a role of microbiota plasticity in the lizards' metabolic adaptation to their resource-constrained insular environments. Overall, our study supports the need for longitudinal and integrative studies of host and associated microbes in natural systems.
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Affiliation(s)
- Laura Baldo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain,Institute for Research on Biodiversity (IRBio), Barcelona, Spain
| | - Giacomo Tavecchia
- Animal Demography and Ecology Unit, IMEDEA, Consejo Superior de Investigaciones Científicas, Esporles, Spain
| | - Andreu Rotger
- Animal Demography and Ecology Unit, IMEDEA, Consejo Superior de Investigaciones Científicas, Esporles, Spain
| | - José Manuel Igual
- Animal Demography and Ecology Unit, IMEDEA, Consejo Superior de Investigaciones Científicas, Esporles, Spain
| | - Joan Lluís Riera
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
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Cicala F, Cisterna-Céliz JA, Paolinelli M, Moore JD, Sevigny J, Rocha-Olivares A. The Role of Diversity in Mediating Microbiota Structural and Functional Differences in Two Sympatric Species of Abalone Under Stressed Withering Syndrome Conditions. MICROBIAL ECOLOGY 2023; 85:277-287. [PMID: 35064808 DOI: 10.1007/s00248-022-01970-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Withering syndrome (WS) is a gastro-intestinal (GI) infectious disease likely affecting all abalone species worldwide. Structural and functional changes in abalone GI microbiotas under WS-stressed conditions remain poorly investigated. It is unclear if interspecific microbiota differences, such as the presence of certain microbes, their abundance, and functional capabilities, may be involved in the occurrence of this disease. Bacterial microbiotas of healthy Haliotis fulgens and Haliotis corrugata are mainly composed by Tenericutes, Proteobacteria, Fusobacteria, and Spirochaetes. We previously reported species-specific structural and functional profiles of those communities and suggested that they are of consequence to the different susceptibility of each species to WS. Here, we address this question by comparing the structure and function of healthy and dysbiotic microbiota through 454 pyrosequencing and PICRUSt 2, respectively. Our findings suggest that the extent to which WS-stressed conditions may explain structural and functional differences in GI microbiota is contingent on the microbiota diversity itself. Indeed, microbiota differences between stressed and healthy abalone were marginal in the more complex bacterial communities of H. corrugata, in which no significant structural or functional changes were detected. Conversely, significant structural changes were observed in the less complex bacterial microbiota of H. fulgens. Moreover, structural alterations led to a significant downregulation of some metabolic activities conducted by GI bacteria. Accordingly, results suggest that gastro-intestinal bacterial diversity appears to be related with both the health of abalone and the etiology of WS.
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Affiliation(s)
- Francesco Cicala
- Department of Biological Oceanography, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico
- Department of Biomedical Innovation, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico
| | | | - Marcos Paolinelli
- National Council of Scientific and Technical Research (CONICET), Av. Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina
- National Institute of Agricultural Technology INTA EEA Mendoza, San Martin 3853, Luján de Cuyo, 5507, Mendoza, Argentina
| | - James D Moore
- Bodega Marine Laboratory, University of California at Davis, P.O. Box 247, Bodega Bay, CA, USA
| | - Joseph Sevigny
- Hubbard Center for Genome Studies, University of New Hampshire, 35 Colovos Rd, Durham, NH, 03824, USA
| | - Axayácatl Rocha-Olivares
- Department of Biological Oceanography, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico.
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36
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Juottonen H, Moghadam NN, Murphy L, Mappes J, Galarza JA. Host's genetic background determines the outcome of reciprocal faecal transplantation on life-history traits and microbiome composition. Anim Microbiome 2022; 4:67. [PMID: 36564793 PMCID: PMC9789590 DOI: 10.1186/s42523-022-00210-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Microbes play a role in their host's fundamental ecological, chemical, and physiological processes. Host life-history traits from defence to growth are therefore determined not only by the abiotic environment and genotype but also by microbiota composition. However, the relative importance and interactive effects of these factors may vary between organisms. Such connections remain particularly elusive in Lepidoptera, which have been argued to lack a permanent microbiome and have microbiota primarily determined by their diet and environment. We tested the microbiome specificity and its influence on life-history traits of two colour genotypes of the wood tiger moth (Arctia plantaginis) that differ in several traits, including growth. All individuals were grown in the laboratory for several generations with standardized conditions. We analyzed the bacterial community of the genotypes before and after a reciprocal frass (i.e., larval faeces) transplantation and followed growth rate, pupal mass, and the production of defensive secretion. RESULTS After transplantation, the fast-growing genotype grew significantly slower compared to the controls, but the slow-growing genotype did not change its growth rate. The frass transplant also increased the volume of defensive secretions in the fast-growing genotype but did not affect pupal mass. Overall, the fast-growing genotype appeared more susceptible to the transplantation than the slow-growing genotype. Microbiome differences between the genotypes strongly suggest genotype-based selective filtering of bacteria from the diet and environment. A novel cluster of insect-associated Erysipelotrichaceae was exclusive to the fast-growing genotype, and specific Enterococcaceae were characteristic to the slow-growing genotype. These Enterococcaceae became more prevalent in the fast-growing genotype after the transplant, which suggests that a slower growth rate is potentially related to their presence. CONCLUSIONS We show that reciprocal frass transplantation can reverse some genotype-specific life-history traits in a lepidopteran host. The results indicate that genotype-specific selective filtering can fine-tune the bacterial community at specific life stages and tissues like the larval frass, even against a background of a highly variable community with stochastic assembly. Altogether, our findings suggest that the host's genotype can influence its susceptibility to being colonized by microbiota, impacting key life-history traits.
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Affiliation(s)
- Heli Juottonen
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Neda N. Moghadam
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Liam Murphy
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Johanna Mappes
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland ,grid.7737.40000 0004 0410 2071Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikki Biocenter 3, 00014 Helsinki, Finland
| | - Juan A. Galarza
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland ,grid.7737.40000 0004 0410 2071Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikki Biocenter 3, 00014 Helsinki, Finland
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Wang Z, Zhang C, Li G, Yi X. The influence of species identity and geographic locations on gut microbiota of small rodents. Front Microbiol 2022; 13:983660. [PMID: 36532505 PMCID: PMC9751661 DOI: 10.3389/fmicb.2022.983660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/10/2022] [Indexed: 10/29/2023] Open
Abstract
Although the correlation between gut microbiota, species identity and geographic locations has long attracted the interest of scientists, to what extent species identity and geographic locations influence the gut microbiota assemblages in granivorous rodents needs further investigation. In this study, we performed a survey of gut microbial communities of four rodent species (Apodemus agrarius, A. peninsulae, Tamias sibiricus and Clethrionomys rufocanus) distributed in two areas with great distance (> 600 km apart), to assess if species identity dominates over geographic locations in shaping gut microbial profiles using 16S rRNA gene sequencing. We found that gut microbiota composition varied significantly across host species and was closely correlated with host genetics. We identified strong species identity effects on gut microbial composition, with a comparatively weaker signal of geographic provenance on the intestinal microbiota. Specifically, microbiota of one species was on average more similar to that of conspecifics living in separate sites than to members of a closely related species living in the same location. Our study suggests that both host genetics and geographical variations influence gut microbial diversity of four rodent species, which merits further investigation to reveal the patterns of phylogenetic correlation of gut microbial community assembly in mammals across multiple habitats.
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Affiliation(s)
- Zhenyu Wang
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Chao Zhang
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Guoliang Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xianfeng Yi
- College of Life Sciences, Qufu Normal University, Qufu, China
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Response of Intestinal Microbiota to the Variation in Diets in Grass Carp (Ctenopharyngodon idella). Metabolites 2022; 12:metabo12111115. [PMID: 36422256 PMCID: PMC9698803 DOI: 10.3390/metabo12111115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 11/17/2022] Open
Abstract
The intestinal microbiota is important for the nutrient metabolism of fish and is significantly influenced by the host’s diet. The effect of ryegrass and commercial diets on the intestinal microbiota of grass carp was compared in this study. In comparison to ryegrass, artificial feed significantly reduced the microbial diversity in the intestine, which was measured by a decrease in the observed OTUs, ACE, Shannon, and the InvSimpson index. Although grass carp fed with ryegrass and artificial feed shared a dominant phyla Firmicutes and Proteobacteria, the microbial composition was clearly distinguishable between the two groups. In grass carp fed with ryegrass, Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria predominated, whereas Bacilli was significantly higher in the artificial feed group due to an increase in Weissella and an unassigned Bacillales bacteria, as well as a significant increase in a potential pathogen: Aeromonas australiensis. Grass carp fed with ryegrass exhibited a more complex ecological network performed by the intestinal bacterial community, which was dominated by cooperative interactions; this was also observed in grass carp fed with artificial feed. Despite this, the increase in A. australiensis increased the competitive interaction within this ecological network, which contributed to the vulnerable perturbation of the intestinal microbiota. The alteration of the microbial composition through diet can further affect microbial function. The intestinal microbial function in grass carp fed with ryegrass was rich in amino acids and exhibited an increased energy metabolism in order to compensate for a low-nutrient diet intake, while the artificial feed elevated the microbial lipid metabolism through the promotion of its synthesis in the primary and secondary bile acids, together with a notable enhancement of fatty acid biosynthesis. These results indicated that diet can affect the homeostasis of the intestinal microbiota by altering the microbial composition and the interspecific interactions, whilst microbial function can respond to a variation in diet.
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Mallott EK. Individualized composition or community dynamics? A new statistical approach to assess the individuality of host-associated microbiomes. Proc Biol Sci 2022; 289:20221794. [PMID: 36350214 PMCID: PMC9653253 DOI: 10.1098/rspb.2022.1794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Elizabeth K. Mallott
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
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40
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Boesch M, Horvath L, Baty F, Pircher A, Wolf D, Spahn S, Straussman R, Tilg H, Brutsche MH. Compartmentalization of the host microbiome: how tumor microbiota shapes checkpoint immunotherapy outcome and offers therapeutic prospects. J Immunother Cancer 2022; 10:jitc-2022-005401. [PMID: 36343977 PMCID: PMC9644363 DOI: 10.1136/jitc-2022-005401] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
The host microbiome is polymorphic, compartmentalized, and composed of distinctive tissue microbiomes. While research in the field of cancer immunotherapy has provided an improved understanding of the interaction with the gastrointestinal microbiome, the significance of the tumor-associated microbiome has only recently been grasped. This article provides a state-of-the-art review about the tumor-associated microbiome and sheds light on how local tumor microbiota shapes anticancer immunity and influences checkpoint immunotherapy outcome. The direct route of interaction between cancer cells, immune cells, and microbiota in the tumor microenvironment is emphasized and advocates a focus on the tumor-associated microbiome in addition to the spatially separated gut compartment. Since the mechanisms underlying checkpoint immunotherapy modulation by tumor-associated microbiota remain largely elusive, future research should dissect the pathways involved and outline strategies to therapeutically modulate microbes and their products within the tumor microenvironment. A more detailed knowledge about the mechanisms governing the composition and functional quality of the tumor microbiome will improve cancer immunotherapy and advance precision medicine for solid tumors.
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Affiliation(s)
| | - Lena Horvath
- Department of Internal Medicine V (Hematology and Oncology) and Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
| | - Florent Baty
- Lung Center, Cantonal Hospital St.Gallen, St.Gallen, Switzerland
| | - Andreas Pircher
- Department of Internal Medicine V (Hematology and Oncology) and Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
| | - Dominik Wolf
- Department of Internal Medicine V (Hematology and Oncology) and Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
| | - Stephan Spahn
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Herbert Tilg
- Department of Internal Medicine I (Gastroenterology, Hepatology, Endocrinology & Metabolism), Medical University of Innsbruck, Innsbruck, Austria
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Manus MB. Ecological Processes and Human Behavior Provide a Framework for Studying the Skin Microbial Metacommunity. MICROBIAL ECOLOGY 2022; 84:689-702. [PMID: 34636925 DOI: 10.1007/s00248-021-01884-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Metacommunity theory dictates that a microbial community is supported both by local ecological processes and the dispersal of microbes between neighboring communities. Studies that apply this perspective to human-associated microbial communities are thus far limited to the gut microbiome. Yet, the skin serves as the primary barrier between the body and the external environment, suggesting frequent opportunities for microbial dispersal to the variable microbial communities that are housed across skin sites. This paper applies metacommunity theory to understand the dispersal of microbes to the skin from the physical and social environment, as well as between different skin sites on an individual's body. This includes highlighting the role of human behavior in driving microbial dispersal, as well as shaping physiological properties of skin that underscore local microbial community dynamics. By leveraging data from research on the skin microbiomes of amphibians and other animals, this paper provides recommendations for future research on the skin microbial metacommunity, including generating testable predictions about the ecological underpinnings of the skin microbiome.
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Affiliation(s)
- Melissa B Manus
- Department of Anthropology, Northwestern University, Evanston, IL, USA.
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42
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Gallet A, Yao EK, Foucault P, Bernard C, Quiblier C, Humbert JF, Coulibaly JK, Troussellier M, Marie B, Duperron S. Fish gut-associated bacterial communities in a tropical lagoon (Aghien lagoon, Ivory Coast). Front Microbiol 2022; 13:963456. [PMID: 36246274 PMCID: PMC9556852 DOI: 10.3389/fmicb.2022.963456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Aghien lagoon (Ivory Coast) is a eutrophic freshwater lagoon that harbors high biomasses of phytoplankton. Despite Increasing interest in fish gut microbiomes diversity and functions, little data is currently available regarding wild species from tropical west African lakes. Here, gut-associated bacterial communities are investigated in four fish species that are consumed by locale populations, namely the Cichlidae Hemichromis fasciatus, Tilapia guineensis and Sarotherodon melanotheron, and the Claroteidae Chrysichthys nigrodigitatus. Species-related differences are identified, that can be attributed to host phylogeny and diet. Important variations throughout the year are observed in T. guineensis and C. nigrodigitatus. This result emphasized the importance of time-series sampling and comparison with environmental variables even in tropical regions, that are not often conducted in wild populations. Effects of environmental factors (anthropogenic or not) on the microbiota and potential outcomes for fish health and populations sustainability need to be further explored. Interestingly, fish appear as major reservoirs of bacterial diversity, suggesting that they could contribute to the overall stability and resilience of bacterial communities present in the Aghien lagoon.
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Affiliation(s)
- Alison Gallet
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Eric Kouamé Yao
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- Institut Pasteur de Côte d’Ivoire, Abidjan, Côte d’Ivoire
| | - Pierre Foucault
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Catherine Quiblier
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- Université Paris Cité, UFR Sciences du Vivant, Paris, France
| | | | | | - Marc Troussellier
- MARBEC, Centre National de la Recherche Scientifique, Université Montpellier, IFREMER, IRD, Montpellier, France
| | - Benjamin Marie
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Sébastien Duperron
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- *Correspondence: Sébastien Duperron,
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Baniel A, Petrullo L, Mercer A, Reitsema L, Sams S, Beehner JC, Bergman TJ, Snyder-Mackler N, Lu A. Maternal effects on early-life gut microbiota maturation in a wild nonhuman primate. Curr Biol 2022; 32:4508-4520.e6. [PMID: 36099914 DOI: 10.1016/j.cub.2022.08.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022]
Abstract
Early-life microbial colonization is an important process shaping host physiology,1-3 immunity,4-6 and long-term health outcomes7-10 in humans. However, our understanding of this dynamic process remains poorly investigated in wild animals,11-13 where developmental mechanisms can be better understood within ecological and evolutionarily relevant contexts.11,12 Using one of the largest developmental datasets on a wild primate-the gelada (Theropithecus gelada)-we used 16S rRNA amplicon sequencing to characterize gut microbiota maturation during the first 3 years of life and assessed the role of maternal effects in shaping offspring microbiota assembly. In contrast to recent data on chimpanzees, postnatal microbial colonization in geladas was highly similar to humans:14 microbial alpha diversity increased rapidly following birth, followed by gradual changes in composition until weaning. Dietary changes associated with weaning (from milk- to plant-based diet) were the main drivers of shifts in taxonomic composition and microbial predicted functional pathways. Maternal effects were also an important factor influencing the offspring gut microbiota. During nursing (<12 months), offspring of experienced (multi-time) mothers exhibited faster functional microbial maturation, likely reflecting the general faster developmental pace of infants born to these mothers. Following weaning (>18 months), the composition of the juvenile microbiota tended to be more similar to the maternal microbiota than to the microbiota of other adult females, highlighting that maternal effects may persist even after nursing cessation.15,16 Together, our findings highlight the dynamic nature of early-life gut colonization and the role of maternal effects in shaping this trajectory in a wild primate.
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Affiliation(s)
- Alice Baniel
- Center for Evolution and Medicine, Arizona State University, E Tyler Mall, Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, E Tyler Mall, Tempe, AZ 85287, USA.
| | - Lauren Petrullo
- Department of Psychology, University of Michigan, Church St., Ann Arbor, MI 48109, USA
| | - Arianne Mercer
- Department of Psychology, University of Washington, Okanogan Ln., Seattle, WA 98195, USA
| | - Laurie Reitsema
- Department of Anthropology, University of Georgia, Jackson St., Athens, GA 30602, USA
| | - Sierra Sams
- Department of Psychology, University of Washington, Okanogan Ln., Seattle, WA 98195, USA
| | - Jacinta C Beehner
- Department of Psychology, University of Michigan, Church St., Ann Arbor, MI 48109, USA; Department of Anthropology, University of Michigan, S University Ave., Ann Arbor, MI 48109, USA
| | - Thore J Bergman
- Department of Psychology, University of Michigan, Church St., Ann Arbor, MI 48109, USA; Department of Ecology and Evolutionary Biology, University of Michigan, N University Ave., Ann Arbor, MI 48109, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, E Tyler Mall, Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, E Tyler Mall, Tempe, AZ 85287, USA; Department of Psychology, University of Washington, Okanogan Ln., Seattle, WA 98195, USA; School for Human Evolution and Social Change, Arizona State University, Cady Mall, Tempe, AZ 85287, USA.
| | - Amy Lu
- Department of Anthropology, Stony Brook University, Circle Rd., Stony Brook, NY 11794, USA.
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Risely A, Schmid DW, Müller-Klein N, Wilhelm K, Clutton-Brock TH, Manser MB, Sommer S. Gut microbiota individuality is contingent on temporal scale and age in wild meerkats. Proc Biol Sci 2022; 289:20220609. [PMID: 35975437 PMCID: PMC9382201 DOI: 10.1098/rspb.2022.0609] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/01/2022] [Indexed: 12/14/2022] Open
Abstract
Inter-individual differences in gut microbiota composition are hypothesized to generate variation in host fitness-a premise for the evolution of host-gut microbe symbioses. However, recent evidence suggests that gut microbial communities are highly dynamic, challenging the notion that individuals harbour unique gut microbial phenotypes. Leveraging a long-term dataset of wild meerkats, we reconcile these concepts by demonstrating that the relative importance of identity for shaping gut microbiota phenotypes depends on the temporal scale. Across meerkat lifespan, year-to-year variation overshadowed the effects of identity and social group in predicting gut microbiota composition, with identity explaining on average less than 2% of variation. However, identity was the strongest predictor of microbial phenotypes over short sampling intervals (less than two months), predicting on average 20% of variation. The effect of identity was also dependent on meerkat age, with the gut microbiota becoming more individualized and stable as meerkats aged. Nevertheless, while the predictive power of identity was negligible after two months, gut microbiota composition remained weakly individualized compared to that of other meerkats for up to 1 year. These findings illuminate the degree to which individualized gut microbial signatures can be expected, with important implications for the time frames over which gut microbial phenotypes may mediate host physiology, behaviour and fitness in natural populations.
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Affiliation(s)
- Alice Risely
- Institute for Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Dominik W. Schmid
- Institute for Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Nadine Müller-Klein
- Institute for Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Kerstin Wilhelm
- Institute for Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Tim H. Clutton-Brock
- Large Animal Research Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Mammal Research Institute, University of Pretoria, Pretoria, South Africa
- Kalahari Research Trust, Kuruman River Reserve, Northern Cape, South Africa
| | - Marta B. Manser
- Mammal Research Institute, University of Pretoria, Pretoria, South Africa
- Kalahari Research Trust, Kuruman River Reserve, Northern Cape, South Africa
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Simone Sommer
- Institute for Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
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Zhang ZJ, Zheng H. Bumblebees with the socially transmitted microbiome: A novel model organism for gut microbiota research. INSECT SCIENCE 2022; 29:958-976. [PMID: 35567381 DOI: 10.1111/1744-7917.13040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/07/2022] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
Eusocial bumble and honey bees are important pollinators for global ecology and the agricultural economy. Although both the bumble and honey bees possess similar and host-restricted gut microbiota, they differ in aspects of morphology, autonomy, physiology, behavior, and life cycle. The social bee gut bacteria exhibit host specificity that is likely a result of long-term co-evolution. The unique life cycle of bumblebees is key for the acquisition and development of their gut microbiota, and affects the strain-level diversity of the core bacterial species. Studies on bumblebee gut bacteria show that they retain less functional capacity for carbohydrate metabolism compared with that of the honeybee. We discuss the potential roles of the bumblebee gut microbiota against pathogenic threats and the application of host-specific probiotics for bumblebees. Given the advantages of the bumblebee microbiome, including the simple structure and host specificity, and the ease of manipulating bumblebee colonies, we propose that bumblebees may provide a valuable system for understanding the general principles of host-microbe interactions, gut-brain axis, and vertical transmission.
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Affiliation(s)
- Zi-Jing Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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Sun M, Li D, Hua M, Miao X, Su Y, Chi Y, Li Y, Sun R, Niu H, Wang J. Black bean husk and black rice anthocyanin extracts modulated gut microbiota and serum metabolites for improvement in type 2 diabetic rats. Food Funct 2022; 13:7377-7391. [PMID: 35730792 DOI: 10.1039/d2fo01165d] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Black rice and black bean have not yet been fully investigated as healthy foods for their therapeutic effects on type 2 diabetes mellitus (T2DM). In this study, we aimed to evaluate the antidiabetic effects of black rice, black bean husk anthocyanin extracts, and their combination on glycolipid metabolism, gut microbiota, and serum metabolites in T2DM rats. Black bean husk and black rice anthocyanin extracts were administered to T2DM rats by gavage for 4 weeks. The results showed that black rice and black bean husk anthocyanin extracts significantly improved blood glucose, insulin resistance, serum oxidative stress state, lipid metabolism and inflammatory cytokines levels in rats, and alleviated liver damage. Black rice and black bean husk anthocyanin extracts increased the abundance of short-chain fatty acid (SCFA) producing bacteria Akkermansia spp., Phascolarctobacterium spp., Bacteroides spp., and Coprococcus spp., changed the gut microbiota structure; activated AMPK, PI3K, and AKT; inhibited HMGCR, G6pase and PEPCK expression; and inhibited hepatic gluconeogenesis. Moreover, by adjusting the levels of urea, deoxycytidine, L-citrulline, pseudouridine, and other serum metabolites in T2DM rats, the arginine biosynthesis and pyrimidine metabolism pathways were downregulated. The above results indicated that black rice and black bean husk anthocyanin extracts had a significant impact on the development of T2DM.
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Affiliation(s)
- Mubai Sun
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, 130033, Changchun, Jilin, China.
| | - Da Li
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, 130033, Changchun, Jilin, China.
| | - Mei Hua
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, 130033, Changchun, Jilin, China.
| | - Xinyu Miao
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, 130033, Changchun, Jilin, China.
| | - Ying Su
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, 130033, Changchun, Jilin, China.
| | - Yanping Chi
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, 130033, Changchun, Jilin, China.
| | - Yueqiao Li
- Department of International Cooperation, Jilin Academy of Agricultural Sciences, 130033, Changchun, Jilin, China
| | - Ruiyue Sun
- Department of Food Science and Engineering, College of Agriculture, Yanbian University, Yanji, 133000, Jilin, China
| | - Honghong Niu
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, 130033, Changchun, Jilin, China.
| | - Jinghui Wang
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, 130033, Changchun, Jilin, China.
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47
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Microbiomes of microscopic marine invertebrates do not reveal signatures of phylosymbiosis. Nat Microbiol 2022; 7:810-819. [PMID: 35618773 DOI: 10.1038/s41564-022-01125-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 04/12/2022] [Indexed: 01/02/2023]
Abstract
Animals and microorganisms often establish close ecological relationships. However, much of our knowledge about animal microbiomes comes from two deeply studied groups: vertebrates and arthropods. To understand interactions on a broader scale of diversity, we characterized the bacterial microbiomes of close to 1,000 microscopic marine invertebrates from 21 phyla, spanning most of the remaining tree of metazoans. Samples were collected from five temperate and tropical locations covering three marine habitats (sediment, water column and intertidal macroalgae) and bacterial microbiomes were characterized using 16S ribosomal RNA gene sequencing. Our data show that, despite their size, these animals harbour bacterial communities that differ from those in the surrounding environment. Distantly related but coexisting invertebrates tend to share many of the same bacteria, suggesting that guilds of microorganisms preferentially associated with animals, but not tied to any specific host lineage, are the main drivers of the ecological relationship. Host identity is a minor factor shaping these microbiomes, which do not show the same correlation with host phylogeny, or 'phylosymbiosis', observed in many large animals. Hence, the current debate on the varying strength of phylosymbiosis within selected lineages should be reframed to account for the possibility that such a pattern might be the exception rather than the rule.
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48
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Kohl KD, Dieppa-Colón E, Goyco-Blas J, Peralta-Martínez K, Scafidi L, Shah S, Zawacki E, Barts N, Ahn Y, Hedayati S, Secor SM, Rowe MP. Gut Microbial Ecology of Five Species of Sympatric Desert Rodents in Relation to Herbivorous and Insectivorous Feeding Strategies. Integr Comp Biol 2022; 62:237-251. [PMID: 35587374 DOI: 10.1093/icb/icac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/12/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbial communities of mammals provide numerous benefits to their hosts. However, given the recent development of the microbiome field, we still lack a thorough understanding of the variety of ecological and evolutionary factors that structure these communities across species. Metabarcoding is a powerful technique that allows for multiple microbial ecology questions to be investigated simultaneously. Here, we employed DNA metabarcoding techniques, predictive metagenomics, and culture-dependent techniques to inventory the gut microbial communities of several species of rodent collected from the same environment that employ different natural feeding strategies [granivorous pocket mice (Chaetodipus penicillatus); granivorous kangaroo rats (Dipodomys merriami); herbivorous woodrats (Neotoma albigula); omnivorous cactus mice (Peromyscus eremicus), and insectivorous grasshopper mice (Onychomys torridus)]. Of particular interest were shifts in gut microbial communities in rodent species with herbivorous and insectivorous diets, given the high amounts of indigestible fibers and chitinous exoskeleton in these diets, respectively. We found that herbivorous woodrats harbored the greatest microbial diversity. Granivorous pocket mice and kangaroo rats had the highest abundances of the genus Ruminococcus and highest predicted abundances of genes related to the digestion of fiber, representing potential adaptations in these species to the fiber content of seeds and the limitations to digestion given their small body size. Insectivorous grasshopper mice exhibited the greatest inter-individual variation in the membership of their microbiomes, and also exhibited the highest predicted abundances of chitin-degrading genes. Culture-based approaches identified 178 microbial isolates (primarily Bacillus and Enterococcus) capable of degrading cellulose and chitin. We observed several instances of strain-level diversity in these metabolic capabilities across isolates, somewhat highlighting the limitations and hidden diversity underlying DNA metabarcoding techniques. However, these methods offer power in allowing the investigation of several questions concurrently, thus enhancing our understanding of gut microbial ecology.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Etan Dieppa-Colón
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260.,Department of Bacteriology, University of Wisconsin - Madison, Madison WI 53706
| | - José Goyco-Blas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | | | - Luke Scafidi
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Sarth Shah
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Emma Zawacki
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Nick Barts
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Young Ahn
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Stefanie Hedayati
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Stephen M Secor
- Department of Biological Sciences, University of Alabama, Tuscaloosa AL 35487
| | - Matthew P Rowe
- Department of Biological Sciences, University of Oklahoma, Norman OK 73019
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49
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Mueller UG, Linksvayer TA. Microbiome breeding: conceptual and practical issues. Trends Microbiol 2022; 30:997-1011. [PMID: 35595643 DOI: 10.1016/j.tim.2022.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/30/2022] [Accepted: 04/11/2022] [Indexed: 10/18/2022]
Abstract
Microbiome breeding is a new artificial selection technique that seeks to change the genetic composition of microbiomes in order to benefit plant or animal hosts. Recent experimental and theoretical analyses have shown that microbiome breeding is possible whenever microbiome-encoded genetic factors affect host traits (e.g., health) and microbiomes are transmissible between hosts with sufficient fidelity, such as during natural microbiome transmission between individuals of social animals, or during experimental microbiome transplanting between plants. To address misunderstandings that stymie microbiome-breeding programs, we (i) clarify and visualize the corresponding elements of microbiome selection and standard selection; (ii) elucidate the eco-evolutionary processes underlying microbiome selection within a quantitative genetic framework to summarize practical guidelines that optimize microbiome breeding; and (iii) characterize the kinds of host species most amenable to microbiome breeding.
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Affiliation(s)
- Ulrich G Mueller
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Timothy A Linksvayer
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.
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50
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Lu Y, Yuan X, Wang M, He Z, Li H, Wang J, Li Q. Gut microbiota influence immunotherapy responses: mechanisms and therapeutic strategies. J Hematol Oncol 2022; 15:47. [PMID: 35488243 PMCID: PMC9052532 DOI: 10.1186/s13045-022-01273-9] [Citation(s) in RCA: 126] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/20/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota have long been recognized to play a key role in human health and disease. Currently, several lines of evidence from preclinical to clinical research have gradually established that the gut microbiota can modulate antitumor immunity and affect the efficacy of cancer immunotherapies, especially immune checkpoint inhibitors (ICIs). Deciphering the underlying mechanisms reveals that the gut microbiota reprogram the immunity of the tumor microenvironment (TME) by engaging innate and/or adaptive immune cells. Notably, one of the primary modes by which the gut microbiota modulate antitumor immunity is by means of metabolites, which are small molecules that could spread from their initial location of the gut and impact local and systemic antitumor immune response to promote ICI efficiency. Mechanistic exploration provides novel insights for developing rational microbiota-based therapeutic strategies by manipulating gut microbiota, such as fecal microbiota transplantation (FMT), probiotics, engineered microbiomes, and specific microbial metabolites, to augment the efficacy of ICI and advance the age utilization of microbiota precision medicine.
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Affiliation(s)
- Yuting Lu
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Xiangliang Yuan
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Miao Wang
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Zhihao He
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Hongzhong Li
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Ji Wang
- National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China.
| | - Qin Li
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
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